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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctaattcttgattgttgactatgtatgaagtctcagtctaggtttttaattagctacaatggtgatgggctaattgctcaccgcacacctgctcgagcattctttcaatttgaaattaaggcattctacacagatgcatttgaaaacccatcatgaatatatcatgacaaggaatcatatttttcagATATACTCTGAAATGATTGGCAATGTTATGACTGATGCGAGATCCACTGGAAAATACTACCACT

Basic information

species Zea mays
transcript GRMZM2G059151_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 6
gtatctaattcttgattgttgactatgtatgaagtctcagtctaggtttttaattagctacaatggtgatgggctaattgctcaccgcacacctgctcgagcattctttcaatttgaaattaaggcattctacacagatgcatttgaaaacccatcatgaatatatcatgac-aaggaatcatatttttcagATATACTCTGAAATGATTGGCAATGTTATGACTGATGCGAGATCCACTGGAAAATACTACCACT
                                                                                        |   |   | |  |||  | | ||  | |  | | |||| |    |||  |  |   ||     | |||  ||  | | | ||   |   ||| | |||||||||||||||||||||||||||| |||||||||||||||||  | || || || || ||||||||||
---------------------------------------------------------------------------------------taggacattttgcacataatatgaaaatca--tcacggcaataataacaagttgac--gatttttcctcaaaaaagt-taacgattgatccatcttctttttcagATATACTCTGAAATGATTGGTAATGTTATGACTGATGCACGCTCAACCGGGAAGTACTACCACT

upper sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA07G39380.1 (Glycine max), 3'ss of exon 6
gtatctaattcttgattgttgactatgtatgaagtctcagtctaggtttttaattagctacaatggtgatgggctaattgctcaccgcacacctgctcgagcattctttcaatttgaaattaaggcattctacacagatgcatttgaaaacccatcatgaatatatcatgacaaggaatcatatttttcagATATACTCTGAAATGATTGGCAATGTTATGACTGATGCGAGATCCACTGGAAAATACTACCACT
                                                                            ||   |       ||  |  |  ||| |||      |||   ||||    ||  | ||    |||||     |  |   | |     | |  | |   | | | |     | ||||||||  | ||||||||||||||||||||||  |||||  |||| ||||||||||| ||||| |
----------------------------------------------------------------------------atgatttgaaatgcatatttttcagctttcccc---ttttggatta---tatgttgcatgcttgcat-----agtctgacctagtcctctttttatttgaatttaa----tgcagATATATGCAGAAATGATTGGCAATGTTATGATAGATGCTCGATCAACTGGAAAATATTACCATT

upper sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 4
gtatctaattcttgattgttgactatgtatgaagtctcagtctaggtttttaattagctacaatggtgatgggctaattgctcaccgcacacctgctcgagcattctttcaatttgaaattaaggcattctacacagatgcatttgaaaacccatcatgaatatatcatgacaaggaatcatatttttcagATATACTCTGAAATGATTGGCAATGTTATGACTGATGCGAGATCCACTGGAAAATACTACCACT
                                                                            ||   |       ||  | ||  ||| |||      |||   ||||    ||  | ||    |||||     |  |   |     | | |  | |   | | | |     | ||||||||  | ||||||||||||||||||||||  |||||  |||| ||||||||||| ||||| |
----------------------------------------------------------------------------atgatttgaaatgcatattcttcagctttcccc---ttttggatta---tatgttgcatgcctgcat-----agtctgacccagttctctttttatttgaatttaa----tgcagATATATGCAGAAATGATTGGCAATGTTATGATAGATGCTCGATCAACTGGAAAATATTACCATT

upper sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 6
gtatctaattcttgattgttgactatgtatgaagtctcagtctaggtttttaattagctacaatggtgatgggctaattgctcaccgcacacctgctcgagcattctttcaatttgaaattaaggcattctacacagatgcatttgaaaacccatcatgaatatatcatgacaaggaatcatatttttcagATATACTCTGAAATGATTGGCAATGTTATGACTGATGCGAGATCCACTGGAAAATACTACCACT
                                                                            |||||| |  |   |  |  |     |  |||| | ||| | ||     |||  | ||    | |||      ||  ||  |     | | |||  ||       | |  | |||||||| |||||||||||||| ||||||||||  |||||  |||| ||||||||||| ||||| |
----------------------------------------------------------------------------attgctaaatgt-tatataat--gatacccttttagttttacat----acatggtgcatgattacatgacttgact-attttcctctttttatgttaa-------tgtgatgcagATATATTCTGAAATGATTGGAAATGTTATGATAGATGCCCGATCAACTGGAAAATATTACCATT

upper sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 6
gtatctaattcttgattgttgactatgtatgaagtctcagtctaggtttttaattagctacaatggtgatgggctaattgctcaccgcacacctgctcgagcattctttcaatttgaaattaaggcattctacacagatgcatttgaaaacccatcatgaatatatcatgacaaggaatcatatttttcagATATACTCTGAAATGATTGGCAATGTTATGACTGATGCGAGATCCACTGGAAAATACTACCACT
                                                                            |||       ||| |  | ||     |  |||| | ||| | ||     |||  | ||    | |||      ||   | ||   | |   |||   | |  | || |  | |||||||| |||||||||||||| ||||||||||  |||||  |||| ||||||||||| ||||| |
----------------------------------------------------------------------------atttagttttgcatattttct---atacccttttagttttagat----acatggtgcatgattacat-----gact--tgattgttttcctatgtttatgt-taatgtaatgcagATATATTCTGAAATGATTGGAAATGTTATGATAGATGCCCGATCAACTGGAAAATATTACCATT

upper sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT4G04040.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatctaattcttgattgttgactatgtatgaagtctcagtctaggtttttaattagctacaatggtgatgggctaattgctcaccgcacacctgctcgagcattctttcaatttgaaattaaggcattctacacagatgcatttgaaaacccatcatgaatatatcatgacaaggaatcatatttttcagATATACTCTGAAATGATTGGCAATGTTATGACTGATGCGAGATCCACTGGAAAATACTACCACT
                                                                                                        |   | | ||| ||||| | ||||   ||  || ||  |||        ||     |  |  |||     |     |||  | | |||||||||| ||||||||||| ||||||||||  |||||| | ||||| ||||||||||| ||||
-------------------------------------------------------------------------------------------------------gtaagtaactttaaaatttatgcata--acttagttgtcttt------ttatagaagaccttccattttgtgattatatacatgt-agATATACTCAGAAATGATTGGAAATGTTATGATCGATGCGCGTTCCACGGGAAAATACTATCACT

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|148953762|gb|EC899129.2|EC899129
EST:     TGAAATGTAAGGAGGTTCCGACAAGCTTTGGATTTGATACAGCTTGCAAG                         ATATACTCTGAAATGATTGGCAATGTTA
genomic: TGAAATGTAAGGAGGTTCCGACAAGCTTTGGATTTGATACAGCTTGCAAGgtatctaatt ... tatttttcagATATACTCTGAAATGATTGGCAATGTTA
EST: gi|31348678|gb|CD433035.1|CD433035
EST:     TGAAATGTAAGGAGGTTCCGACAAGCTTTGGATTTGATACAGCTTGCAAG                         ATATACTCTGAAATGATTGGCAATGTTATGACTGATGCGAGATCCACTGGA
genomic: TGAAATGTAAGGAGGTTCCGACAAGCTTTGGATTTGATACAGCTTGCAAGgtatctaatt ... tatttttcagATATACTCTGAAATGATTGGCAATGTTATGACTGATGCGAGATCCACTGGA
EST: gi|149103124|gb|EE288493.2|EE288493
EST:     TGAAATGTAAGGAGGTTCCGACAAGCTTTGGATTTGATACAGCTTGCAAG                         ATATACTCTGAAATGATTGGCAATGTTATGACTGATGCGAGATCCACTGGA
genomic: TGAAATGTAAGGAGGTTCCGACAAGCTTTGGATTTGATACAGCTTGCAAGgtatctaatt ... tatttttcagATATACTCTGAAATGATTGGCAATGTTATGACTGATGCGAGATCCACTGGA
EST: gi|6587580|gb|AW244898.1|AW244898
EST:     TGAAATGTAAGGAGGTTCCGACAAGCTTTGGATTTGATACAGCTTGCAAG                         ATATACTCTGAAATGATTGGCAATGTTATGACTGATGCGAGATCCACTGGA
genomic: TGAAATGTAAGGAGGTTCCGACAAGCTTTGGATTTGATACAGCTTGCAAGgtatctaatt ... tatttttcagATATACTCTGAAATGATTGGCAATGTTATGACTGATGCGAGATCCACTGGA
EST: gi|31354738|gb|CD439095.1|CD439095
EST:     TGAAATGTAAGGAGGTTCCGACAAGCTTTGGATTTGATACAGCTTGCAAG                         ATATACTCTGAAATGA
genomic: TGAAATGTAAGGAGGTTCCGACAAGCTTTGGATTTGATACAGCTTGCAAGgtatctaatt ... tatttttcagATATACTCTGAAATGA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 278

GAACATGAAAACCCGTGTTATTGGTTGCCCAAAGACTATCGATGGGGATCTGAAATGTAAGGAGGTTCCGACAAGCTTTGGATTTGATACAGCTTGCAAGgtatctaatt ... tatttttcagATATACTCTGAAATGATTGGCAATGTTATGACTGATGCGAGATCCACTGGAAAATACTACCACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 290

GAACATGAAAACCCGTGTTATTGGTTGCCCAAAGACTATCGATGGGGATCTGAAATGTAAGGAGGTTCCGACAAGCTTTGGATTTGATACAGCTTGCAAGgtatctaatt ... tatttttcagATATACTCTGAAATGATTGGCAATGTTATGACTGATGCGAGATCCACTGGAAAATACTACCACT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 244

GAACATGAAAACCCGTGTTATTGGTTGCCCAAAGACTATCGATGGGGATCTGAAATGTAAGGAGGTTCCGACAAGCTTTGGATTTGATACAGCTTGCAAGgtatctaatt ... tatttttcagATATACTCTGAAATGATTGGCAATGTTATGACTGATGCGAGATCCACTGGAAAATACTACCACT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 341

GAACATGAAAACCCGTGTTATTGGTTGCCCAAAGACTATCGATGGGGATCTGAAATGTAAGGAGGTTCCGACAAGCTTTGGATTTGATACAGCTTGCAAGgtatctaatt ... tatttttcagATATACTCTGAAATGATTGGCAATGTTATGACTGATGCGAGATCCACTGGAAAATACTACCACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgcatttgaaaacccatcatgaatatatcatgacaaggaatcatatttttcagATATACTCTGAAATGATTGGCAATGTTATGACTGATGCGAGATCCACTGGAAAATACTACCACT
                                             tatttttc  CT-rich tract
                                        aatcatatttttca  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatctaattcttgattgttgactatgtatgaagtctcagtctaggtttttaattagctacaatggtgatgggctaattgctcaccgcacacctgctcgagcattctttcaatttgaaattaaggcattctacacagatgcatttgaaaacccatcatgaatatatcatgacaaggaatcatatttttcagATATACTCTGAAATGATTGGCAATGTTATGACTGATGCGAGATCCACTGGAAAATACTACCACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC